Biodiversity conflicts arise when the interests of different stakeholders over common resources compete. Typically, the more parties involved, the more complex situations become. Resolution of biodiversity conflicts requires an understanding of the ecological, social and economic factors involved, in other words the interests and priorities of each stakeholder. However, in most biodiversity conflicts, many of these components remain poorly understood. As a case study, we analyse the conflict involving conservationists, hunters and farmers in the management of a native lagomorph, the European rabbit Oryctolagus cuniculus, in the Iberian Peninsula. We review the socio-economic context of the rabbit management conflict, investigating the roles of the main stakeholders involved in the conflict and evaluating the ecological, economic and social factors that motivate it. We provide management directions for the short-term amelioration of the conflict and discuss some long-term perspectives. Overall, the interests of conservationists, hunters and farmers depend on the specific scenario where the conflict takes place. A deeper understanding of the human dimensions of the conflict will help in the design of an appropriate management model to solve this biodiversity conflict in the Iberian Peninsula.